tbuckley/cabot-search huggingface dataset:
Abstract 1043: Advances in cystine-dense peptide (CDP) screening and therapeutic applications
Authors: Zachary R. Crook, Emily J. Girard, Gregory P. Sevilla, Mi-Youn Brusniak, Peter B. Rupert, Della J. Friend, Mesfin M. Gewe, Midori Clarke, Ida Lin, Raymond Ruff, Doan Phi, Ashok Bandaranayake, Colin E. Correnti, Andrew J. Mhyre, Natalie W. Nairn, Roland K. Strong, James M. Olson
Journal: Cancer Research (2022)

Abstract Cystine-dense peptides (CDPs) are a class of drug-like miniproteins that marry many of the advantages of biologics (high affinity and specificity) and small molecule therapeutics (high tissue permeability and low immunogenicity). The beneficial properties of CDPs, and miniproteins in general, have driven interest in therapeutic applications. However, CDP diversity is vast from every clade of life, and properly interrogating “CDP space” requires specialized screening and modeling tools. With this in mind, we have created an optimized mammalian surface display platform to screen for CDPs of clinical interest using libraries of structurally-diverse native scaffolds optimized for stability. These native CDPs can be structurally modeled, which we did in determining the structures of over 4200 native CDPs. This modeling permits further selection in silico as well as targeted mutagenesis for favorable target-binding capabilities. Hits from these screens are routinely matured to sub-nM affinity. These CDPs can play numerous roles in a drug design pipeline, from an independent drug candidate to a delivery agent for tissue-targeting to a module in a polyspecific biologic. Recent novel CDP candidates have shown promise in immune-oncology space as part of a bispecific T-cell engager targeting PD-L1, where a single 2-week treatment was capable of eliminating subcutaneous PC3 prostate cancer xenograft tumors in 27/30 mice. Besides bispecifics, future directions for the platform include exploring targeted protein degradation. Additionally, we are expanding upon our previous work on CDPs to explore CNS or tumor delivery of therapeutic cargo. The versatility of CDPs and novel screening tools to rapidly identify and mature candidates of interest can facilitate rapid advancement of CDP therapeutics to address difficult targets in oncology. Citation Format: Zachary R. Crook, Emily J. Girard, Gregory P. Sevilla, Mi-Youn Brusniak, Peter B. Rupert, Della J. Friend, Mesfin M. Gewe, Midori Clarke, Ida Lin, Raymond Ruff, Doan Phi, Ashok Bandaranayake, Colin E. Correnti, Andrew J. Mhyre, Natalie W. Nairn, Roland K. Strong, James M. Olson. Advances in cystine-dense peptide (CDP) screening and therapeutic applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1043.
Abstract 6079: Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity
Authors: Yumo Xie, Yu Zhang, Guannan Tang, Xiaolin Wang, Meijin Huang, Yanxin Luo, Huichuan Yu
Journal: Cancer Research (2022)

Abstract Purpose: Intratumoral heterogeneity emerges from accumulating genetic and epigenetic changes during tumorigenesis, which may contribute to therapeutic failure and drug resistance. We aimed to develop a tool that can evaluate the intratumoral epigenetic heterogeneity using the DNA methylation profiles from bulk tumors. Methods: Ggenomic DNA of three laser micro-dissected tumor regions, including digestive tract surface (DTS), central bulk (CB), and invasive margin (IM), was extracted from formalin-fixed paraffin-embedded (FFPE) sections of 98 colorectal cancer patients. The genome-wide methylation profiles were generated with methylation array. The most variable methylated probes were selected to construct a DNA methylation-based heterogeneity (MeHEG) estimation tool that can deconvolve the proportion of each reference tumor region with the support vector machine model-based method. A PCR-based assay for quantitative analysis of DNA methylation (QASM) was developed to specifically determine the methylation status of each CpG in MeHEG assay at single-base resolution to realize fast evaluation of epigenetic heterogeneity. Results: In the discovery set with 79 patients, the differentially methylated CpGs among the three tumor regions were found. The 7 most representative CpGs were identified by random forest analysis and subsequently selected to develop the MeHEG algorithm. We validated its performance of deconvolution of tumor regions in an independent cohort with 19 patients. In addition, we showed the significant association of MeHEG-based epigenetic heterogeneity with the genomic heterogeneity in mutation and copy number variation in our in-house and TCGA cohorts. Finally, we found that the patients with higher MeHEG score had worse disease-free and overall survival outcomes. Conclusion: By constructing a 7-loci panel with a machine learning approach and QASM assay to facilitate its use in a PCR manner, we developed a valuable method to evaluate the intratumoral epigenetic heterogeneity. The MeHEG algorithm provides innovative insights into the intratumoral heterogeneity from the epigenetic perspective that may add valuable sources to current knowledge about tumor heterogeneity. Citation Format: Yumo Xie, Yu Zhang, Guannan Tang, Xiaolin Wang, Meijin Huang, Yanxin Luo, Huichuan Yu. Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6079.
Arthroscopic partial meniscectomy versus physical therapy for traumatic meniscal tears in a young study population: a randomised controlled trial
Authors: Sabine J A van der Graaff, Susanne M Eijgenraam, Duncan E Meuffels, Eline M van Es, Jan A N Verhaar, Dirk Jan Hofstee, Kiem Gie Auw Yang, Julia C A Noorduyn, Ewoud R A van Arkel, Igor C J B van den Brand, Rob P A Janssen, Wai-Yan Liu, Sita M A Bierma-Zeinstra, Max Reijman
Journal: British Journal of Sports Medicine (2022)

Objective To compare outcomes from arthroscopic partial meniscectomy versus physical therapy in young patients with traumatic meniscal tears. Methods We conducted a multicentre, open-labelled, randomised controlled trial in patients aged 18–45 years, with a recent onset, traumatic, MRI-verified, isolated meniscal tear without knee osteoarthritis. Patients were randomised to arthroscopic partial meniscectomy or standardised physical therapy with an optional delayed arthroscopic partial meniscectomy after 3-month follow-up. The primary outcome was the International Knee Documentation Committee (IKDC) score (best 100, worst 0) at 24 months, which measures patients’ perception of symptoms, knee function and ability to participate in sports activities. Results Between 2014 and 2018, 100 patients were included (mean age 35.1 (SD 8.1), 76% male, 34 competitive or elite athletes). Forty-nine were randomised to arthroscopic partial meniscectomy and 51 to physical therapy. In the physical therapy group, 21 patients (41%) received delayed arthroscopic partial meniscectomy during the follow-up period. In both groups, improvement in IKDC scores was clinically relevant during follow-up compared with baseline scores. At 24 months mean (95% CI) IKDC scores were 78 (71 to 84) out of 100 points in the arthroscopic partial meniscectomy group and 78 (71 to 84) in the physical therapy group with a between group difference of 0.1 (95% CI −7.6 to 7.7) points out of 100. Conclusions In this trial involving young patients with isolated traumatic meniscal tears, early arthroscopic partial meniscectomy was not superior to a strategy of physical therapy with optional delayed arthroscopic partial meniscectomy at 24-month follow-up. Trial registration https://www.trialregister.nl/trials .
Abstract 1051: Combination of senaparib with temozolomide for the treatment of cancer
Authors: Sui Xiong Cai, Ning Ma, Xiaozhu Wang, Jie Ma, Mingchuan Guo, Ruiyu Zhou, Lan Liu, Chih-Yi Hsieh, Ye Edward Tian
Journal: Cancer Research (2022)

Abstract Poly (ADP-ribose) polymerase (PARP) is a critical enzyme for DNA repair and PARP inhibitors have been found to be efficacious against cancers with defects in DNA repair pathways such as with BRCA mutations. In addition, in vitro and in vivo studies have found that for PARP inhibitors with good trapping activity, combination with temozolomide (TMZ) produced the best synergetic effects among different types of chemotherapies. Several clinical combination studies of PARP inhibitors with TMZ have been reported, such as the combination of olaparib with TMZ in small cell lung cancer (SCLC). In this presentation, we will report in vitro and in vivo studies of PARP inhibitor senaparib (IMP4297) in combination with TMZ. Synergetic effects were observed when senaparib was combined with TMZ in vitro against human SCLC NCI-H209 cells. In vivo studies of high-dose senaparib in combination with low-dose TMZ once a day continuously in human SCLC NCI-H209 xenograft model was found to be highly synergetic and well tolerated. A clinical study of senaparib in combination with TMZ in patients with advanced solid tumors and SCLC is ongoing (ClinicalTrials.gov Identifier: NCT04434482). Citation Format: Sui Xiong Cai, Ning Ma, Xiaozhu Wang, Jie Ma, Mingchuan Guo, Ruiyu Zhou, Lan Liu, Chih-Yi Hsieh, Ye Edward Tian. Combination of senaparib with temozolomide for the treatment of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1051.
Abstract 3969: Y842 mutations in the activation loop of FLT3 regulates drug response in FLT3-ITD positive acute myeloid leukemia
Authors: Lina Al Ashiri, Sausan Moharram, Rituraj Purohit, Julhash Kazi Uddin, Lars Rönnstrand
Journal: Cancer Research (2022)

Abstract Acute myeloid leukemia (AML) is an aggressive form of blood cancer with a poor prognosis. Approximately 30% of AML patients carry mutations in the type III receptor tyrosine kinase FLT3. The most common form of FLT3 mutations includes internal tandem duplication (ITD) mutations, which are also associated with poor clinical outcomes. Several inhibitors of FLT3 have been developed and are under clinical trials. Major problems in targeting FLT3-ITD include acquired resistance to the inhibitors which is mediated by secondary point mutations in FLT3. The activity of many, but not all, tyrosine kinases is dependent on the well-conserved tyrosine residue in the activation loop for receptor activation. For instance, we have recently shown that the KIT receptor is dependent on its activation loop tyrosine for downstream signaling and receptor stability, but not for the activation of the receptor. In many AML patients, FLT3-ITD mutations in combination with mutations in the activation loop tyrosine residue (Y842) result in drug resistance. We therefore stably transduced cells with FLT3-ITD in combination with different Y842 mutants (Y842C and Y842F). Using MM-PBSA, we found that the introduction of the Y842C and Y842F point mutations changed the binding energy of the FLT3 inhibitors quizartinib, sorafenib, and midostaurin in silico. In addition, the mutants displayed a change in drug response and apoptosis levels after treatments with FLT3 inhibitors in vitro. Previous data from our lab also shows that the Y842F mutant resulted in delayed tumor formation in vivo, indicating that the phosphorylation of the activation loop tyrosine is an important event in FLT3-ITD-mediated transformation. All in all, our data suggest that the activation loop tyrosine residue in FLT3-ITD positive cells plays an important role in drug response and tumor formation. Citation Format: Lina Al Ashiri, Sausan Moharram, Rituraj Purohit, Julhash Kazi Uddin, Lars Rönnstrand. Y842 mutations in the activation loop of FLT3 regulates drug response in FLT3-ITD positive acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3969.
Abstract 5201: Enhanced production of IL-2 from anti CD3-stimulated mouse spleen cells by artepillin C, a major component of Brazilian green propolis
Authors: Nobuo Kondoh, Masako Kamiya, Hanemi Tsuruta, Moe Takahashi, Kumiko Ikeno, Kyohei Ueno, Naoki Umemura, Eiji Takayama, Harumi Kawaki, Genjiro Nakamura, Toru Nikaido, Yasunori Muramatsu, Megumi Ando
Journal: Cancer Research (2022)

Abstract Objectives: It has been reported that Brazilian green propolis (BGP) possesses anti-tumor and chemo-preventive properties against prostate cancer (Szliszaka E, 2011). And bioactive components from propolis have been shown to have anti-cancerous effects upon hepatocellular carcinoma (Liu X, 2021). These observations revealed that propolis can be an anti-cancer drugs, however the immunological effects upon tumor microenvironments of these naturally occurring components has not been elucidated. In this report, we attempt to clarify immune modulatory effects of BGP and the major component, artepillin C, by observing cytokine production from activated T cells. Methods: The mouse spleen cell stimulated by anti-CD3 monoclonal antibody were co-cultured with BGP, artepillin C and HC030031, an antagonist of TRPA1 Ca2+ channel. The productions of IFN-γ, IL-6, IL-17, IL-4, IL-10 and IL-2 was assayed by ELISA. Results: Our results demonstrated the production of IL-2 was markedly enhanced, while the production of IL-4 and IL-10 was not significantly affected; by contrast, the production of IFN-γ, IL-6 and IL-17 were markedly reduced, in the highly viable stimulated spleen cells treated with BGP. These effects were also reproduced in the cells treated with artepillin C, a major component of BGP. The enhancement of IL-2 production by artepillin C was significantly alleviated by adding 10 HC030031, an antagonist of TRPA1 Ca2+ channel, suggesting the enhancement of the cytokine production by artepillin C could be mediated by Ca2+ influx. Conclusions: The artepillin C, a major component of BGP, is an important regulator of activated T lymphocytes and specifically augmented the expression of IL-2 vie Ca2+-permeable cation channel, TRPA1. These effects may exert immunomodulatory effects upon tumor microenvironments. Citation Format: Nobuo Kondoh, Masako Kamiya, Hanemi Tsuruta, Moe Takahashi, Kumiko Ikeno, Kyohei Ueno, Naoki Umemura, Eiji Takayama, Harumi Kawaki, Genjiro Nakamura, Toru Nikaido, Yasunori Muramatsu, Megumi Ando. Enhanced production of IL-2 from anti CD3-stimulated mouse spleen cells by artepillin C, a major component of Brazilian green propolis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5201.
Abstract 659: Mechanisms of resistance to SHP2 inhibition
Authors: Wei Wei, Mitchell Geer, Xinyi Guo, Neville Sanjana, Benjamin G. Neel
Journal: Cancer Research (2022)

Abstract SHP2 (PTPN11) is required for RAS activation, acting upstream of SOS1/2. Allosteric SHP2 inhibitors (SHP2is) stabilize auto-inhibition mediated by N-SH2/PTP interactions and prevent its activation by upstream stimuli. SHP2is impair the proliferation of oncogenic RTK- or cycling RAS mutant-expressing tumor cells and can overcome adaptive resistance to single agents targeting the RAS-MAPK-ERK pathway (e.g., EGFR, KRASG12C, BRAFV600E, MEK inhibitors). Multiple SHP2is are in clinical trials as single agents or in various combinations. As resistance to targeted therapy is universal, we sought to prospectively identify potential SHP2-extrinsic resistance mechanisms by performing genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive human FLT3-ITD driven AML cell lines, MOLM13 and MV4:11. We identified several expected “hits” based on known signaling pathways, including tumor suppressor (NF1, PTEN,CDKN1B) and “RASopathy” (LZTR1, RASA2) genes, as well as novel targets including INPPL1,MAP4K5, and some epigenetic modifiers. To test the generality of these findings, we built a“mini-CRISPR library of ~30 hits common to MOLM13 and MV4:11 cells and screened 15 SHP2i-sensitive lines. LZTR1 deletion conferred resistance in 14/15, followed by MAP4K5 (9/15),SPRED2 (6/15), STK40 (6/15), INPPL1 (5/15), NCOA6 (4/15), NCOR1 (4/15), and ELAVL1 (4/15). LZTR1 has been reported to regulate RIT or RAS stability. Notably, LZTR1 knockout universally increased RIT1, but in some lines, also increased RAS. INPPL1 encodes SHIP2, a 5’-inositide phosphatase that negatively regulates AKT activation in insulin signaling. However, INPPL1 deletion also increased RAS and ERK activity and activated ERK-dependent genes in FLT3-ITD AML lines. Experiments with INPPL1 mutant showed that SHC binding and an N-terminal region, but not the SH2 domain or phosphatase activity, is required for negative regulation of RAS. Interestingly, INPPL1 deletion also promoted resistance to SHP2 inhibition in several EGFR mutant cell lines. MAP4K5 deletion also increased ERK-dependent gene expression. Kinase activity, but not JNK activation, was required for MAP4K5 action. Our results predict multiple mechanisms of SHP2i resistance, emphasizing the need for detailed understanding of the resistance landscape to arrive a combinations that provide long term disease control. Citation Format: Wei Wei, Mitchell Geer, Xinyi Guo, Neville Sanjana, Benjamin G. Neel. Mechanisms of resistance to SHP2 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 659.
Abstract 918: Development of a platform for programmable <i>in vivo</i> oncogene activation and screening using CRISPRa technology
Authors: Fredrik Ivar Thege, Dhwani N. Rupani, Bhargavi B. Barathi, Anirban Maitra, Andrew D. Rhim, Sonja M. Wörmann
Journal: Cancer Research (2022)

Abstract Conventional genetically engineered mouse models (GEMMs) are time consuming, laborious and offer limited spatio-temporal control. We have developed a streamlined platform for in vivo gene activation using CRISPR activation (CRISPRa) technology. Our model system allows for flexible, sustained and timed activation of one or more target genes, in vitro or in vivo, using single or pooled lentiviral guides. Using Myc and Yap1 as model oncogenes, we implemented this platform to study the effect of oncogene activation on the tumorigenic potential of primary pancreatic organoids, as well as in an autochthonous model of lung adenocarcinoma. We found that Myc-activation in pancreatic organoids increased their tumorigenic potential and resulted in significantly shorter survival relative to controls when transplanted orthotopically. In vivo Myc activation in the lung accelerated tumor progression and resulted in significantly shorter overall survival relative to non-targeted tumor controls. Furthermore, we found that Myc-activation drives the acquisition of an immune suppressive “cold” tumor microenvironment. Through cross-species validation of our results, we were able to link MYC to a previously described, immunosuppressive transcriptomic subtype in patient tumors, thus identifying a patient cohort that may benefit from combined MYC/immune-targeted therapies. Our work demonstrates how CRISPRa can be used for rapid functional validation of putative oncogenes and may allow for the identification and evaluation of potential metastatic and oncogenic drivers through competitive screening. Citation Format: Fredrik Ivar Thege, Dhwani N. Rupani, Bhargavi B. Barathi, Anirban Maitra, Andrew D. Rhim, Sonja M. Wörmann. Development of a platform for programmable in vivo oncogene activation and screening using CRISPRa technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 918.
Abstract 5227: Combination therapy activating the integrated stress response synergistically suppresses proliferation and induces apoptosis in diffuse intrinsic pontine glioma
Authors: Orlandi V. Novak, Antje Arnold, Charles Eberhart, Eric H. Raabe
Journal: Cancer Research (2022)

Abstract Diffuse intrinsic pontine glioma (DIPG) is a lethal pediatric brain tumor. Radiation, the standard of care, extends life for 6-18 months but has never cured a patient. Therefore, the discovery of novel treatments is imperative. DIPG tumors have elevated baseline activation of the integrated stress response (ISR), an evolutionarily conserved system that allows cells to tolerate various forms of stress. Increased expression of activating transcription factor 4 (ATF4) indicates activation of the ISR. Low levels of ATF4 protect cells from stress, while sustained high-levels of ATF4 result in cell death. Because DIPG has a high baseline level of ATF4, we hypothesized that the ISR activators Sal003 and ONC201 would synergize and kill DIPG cells. After determining the IC25 of Sal003 and ONC201, we treated three patient-derived cell lines: JHH-DIPG1, SF-7761, and JHH-DIPG16A with low micromolar doses. To measure proliferation, we performed immunofluorescence staining for bromodeoxyuridine (BrdU) incorporation. The combination treatment significantly reduced BrdU incorporation (JHH-DIPG1 p=0.0026, SF-7761 p=0.0002, JHH-DIPG16A p&amp;lt;0.0001 by ANOVA and Dunnett’s multiple comparisons test compared to DMSO control). In all three cell lines, the combination also significantly reduced proliferation compared to monotherapy. We next measured apoptosis by staining for cleaved caspase-3 (CC3) and performing western blots for cleaved PARP. The combination of Sal003 and ONC201 significantly increased apoptosis as measured by CC3 immunofluorescence in comparison to DMSO (JHH-DIPG1 p&amp;lt;0.0001, SF-7761 p&amp;lt;0.0001, JHH-DIPG16A p&amp;lt;0.0001 by ANOVA and Dunnett’s multiple comparisons test compared to DMSO control). In all cell lines, combination therapy significantly increased CC3 positivity compared to single treatment. Western blots for cleaved PARP expression detected induction of apoptosis in all three cell lines treated with the combination over DMSO and monotherapy treated cells. In JHH-DIPG1 and SF-7761, the combination increased ATF4 expression. Since Sal003 is not yet available for clinical testing in humans, we will next investigate treatment with ONC201 and the well-tolerated ATF4 inducer fenretinide. The combination of ONC201 with another ISR activating agent has the potential to serve as a therapy for DIPG. Citation Format: Orlandi V. Novak, Antje Arnold, Charles Eberhart, Eric H. Raabe. Combination therapy activating the integrated stress response synergistically suppresses proliferation and induces apoptosis in diffuse intrinsic pontine glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5227.